[BioC] Converting data into MAlist to use in LIMMA

[stephen sefick]

The convert package is a bioconductor package and I think the function
that you want is

as(foo, "MAlist")

On Wed, Feb 10, 2010 at 12:40 PM, Aubin-Horth Nadia
<Nadia.Aubin-Horth at bio.ulaval.ca> wrote:
> HI everybody
>
> We conducted a two-color microarray experiment using a 19 000-probe home
> made cDNA array. Our experiment contains 12 arrays. We use LIMMA to do all
> the normalization and model fitting and stats. Out of the 19 000 probes,
> several clones are part of the same contig, as annotated by TIGR. We decided
> to average the M values for these clones that correspond to a single contig
> to obtain a single M value for a given contig, for each array separately. We
> also wanted to remove probes that were called empty after sequencing (but
> they were already on the printed microarray). We exported the MAlist
> containing the normalised data (called "MAptip.nba.scale") and extracted the
> M data for each of the 12 slides in Python. We did the averaging and
> removing of "empty" spots and now have a new file with columns containing
> information on block, row, column, spot ID, annotation information for the
> contigs (and singletons) and then data for each slide in the following
> columns. Each row contains the averaged M values.
>
> We looked for a way to convert this file back into a MAlist so we can
> specify our design and do a fit. We read in the archives about a library
> called convert (which we did not find on CRAN) and info on how to transform
> data into an exprSet for affy data. Would someone be willing to help us with
> this task and give us pointers?
>
> Thank you very much
>
> Nadia Aubin-Horth
> Assistant professor
> Biology Department
> Institute of Integrative and Systems Biology
> Université Laval
> Québec, Canada
>
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-- 
Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis